def movemap(pose, PDB_out=False):
"""
Demonstrates the syntax necessary for basic usage of the MoveMap object
performs these changes with a demonstrative backbone minimization
using <pose> and writes structures to PDB files if <PDB_out> is True
"""
#########
# MoveMap
# a MoveMap encodes what data is allowed to change in a Pose, referred to as
# its degrees of freedom
# a MoveMap is separate from a Pose and is usually required by a Mover so
# that the correct degrees of freedom are manipulated, in this way,
# MoveMap and Pose objects often work in parallel
# several MoveMap's can correspond to the same Pose
# a MoveMap stores information on a per-residue basis about the
# backbone ({phi, psi, omega}) and chi ({chi_i}) torsion angle sets
# the MoveMap can only set these sets of torsions to True or False, it
# cannot set freedom for the individual angles (such as phi free and psi
# fixed)
# the MoveMap has no upper-limit on its residue information, it defaults to
# all residues (up to residue 99999999) backbone and chi False
# you can view the MoveMap per-residue torsion settings by using the
# MoveMap.show( Pose.total_residue() ) method (the input argument is the
# highest residue to output, it does not support viewing a range)
pose_move_map = MoveMap()
# change all backbone torsion angles
pose_move_map.set_bb(True)
# change all chi angle torsion angles (False by default)
pose_move_map.set_chi(False)
# change a single backbone torsion angles
#pose_move_map.set_bb(1, True) # example syntax
# change a single residue's chi torsion angles
#pose_move_map.set_chi(1, True) # example syntax
pose_move_map.show(pose.total_residue())
# perform gradient based minimization on the "median" residues, this
# method (MinMover) determines the gradient of an input pose using a
# ScoreFunction for evaluation and a MoveMap to define the degrees of
# freedom
# create a standard ScoreFunction
scorefxn = get_fa_scorefxn(
) # create_score_function_ws_patch('standard', 'score12')
# redefine the MoveMap to include the median half of the residues
# turn "off" all backbone torsion angles
pose_move_map.set_bb(False) # reset to backbone False
# turn "on" a range of residue backbone torsion angles
pose_move_map.set_bb_true_range(int(pose.total_residue() / 4),
int(pose.total_residue() * 3 / 4))
# create the MinMover
minmover = protocols.minimization_packing.MinMover()
minmover.score_function(scorefxn)
minmover.movemap(pose_move_map)
# create a copy of the pose
test_pose = Pose()
test_pose.assign(pose)
# apply minimization
scorefxn(test_pose) # to prevent verbose output on the next line
pymover = PyMOLMover()
#### uncomment the line below and "comment-out" the two lines below to
#### export the structures into different PyMOL states of the same object
#pymover.keep_history = True # enables viewing across states
#### comment-out the line below, changing PDBInfo names tells the
#### PyMOLMover to produce new objects
test_pose.pdb_info().name('original')
pymover.apply(test_pose)
print('\nPre minimization score:', scorefxn(test_pose))
minmover.apply(test_pose)
if PDB_out:
test_pose.dump_pdb('minimized.pdb')
print('Post minimization score:', scorefxn(test_pose))
#### comment-out the line below
test_pose.pdb_info().name('minimized')
pymover.apply(test_pose)
print('Refinement ----------------------------------------------')
kT = 1.0
n_moves = 10
pose = core.import_pose.pose_from_file("../test/data/test_fragments.pdb")
pose_frag = core.import_pose.pose_from_file("../test/data/test_fragments.pdb")
print('setting up a move map')
movemap = MoveMap()
print('setting all backbone movement to true, and residue 10 to false')
movemap.set_bb(True)
movemap.set_bb(10, False)
print('outputting movemap')
movemap.show(pose.total_residue())
fragset3mer = core.fragment.ConstantLengthFragSet(
3, "../test/data/test3_fragments") # "aatestA03_05.200_v1_3")
fragset9mer = core.fragment.ConstantLengthFragSet(
9, "../test/data/test9_fragments") # "aatestA09_05.200_v1_3")
print('mover: ClassicFragmentMover, 3mer')
movemap.set_bb(True)
mover_3mer = protocols.simple_moves.ClassicFragmentMover(fragset3mer, movemap)
mover_3mer.apply(pose_frag)
print('Creating standard score function with patch and scoring')
scorefxn = get_score_function()
scorefxn(pose)
print('mover: SmallMover')